Tool for BAM coverage without the soft clipping base

Question

[nayshool]

Hi everyone,

I am looking for a software/script which calculate the mean coverage of an area without the soft clipping bases. It's exclude the soft/hard clipping bases and leave only the true annotated bases in the calculation.

thank you

Answer 1

[Devon Ryan]

Almost anything that produces coverage metrics will do what you're describing. As an example, you can use bamCoverage or multiBamSummary from deepTools to do this, though other common choices would be bedtools or even featureCounts.

[nayshool]

I don't want to count the soft clipping reads. Are those software will not count them?

[Devon Ryan]

Correct, none of those (or even samtools view -c) will count soft-clipped portions of reads.

Answer 2

[Pierre Lindenbaum]

GATK depthofcoverage: https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php

In most (all?) tools the clipping section is ignored.